predict patient from k mds coordinates and accuracy

predictPatient.R

j = unlist(locals[2:3])
obj2 = obj[,j]
sampleID2 = sampleID[j]

mat = MRcounts(obj2,norm=TRUE,log=TRUE)
otusToKeep <- which(rowSums(mat)>0)
otuVars<-rowSds(mat[otusToKeep,])
otuIndices<-otusToKeep[order(otuVars,decreasing=TRUE)[1:1000]]
mat <- mat[otuIndices,]
mat = t(mat)
d <- dist(mat)
ord = cmdscale(d,k=10)

cl = factor(as.character(sampleID2))

# Arbitrarily chose 10 cooridnates
x = lda(ord[,1:10],grouping=cl,CV=TRUE)
x = x$post # posterior probs
kk = which(is.na(rowSums(x)))
x = x[-kk,]
cl = cl[-kk]

pred = sapply(1:nrow(x),function(i){
    names(which(x[i,]==rowMax(x)[i]))
})
combo = cbind(truth = as.character(cl),pred)
sum(combo[,1]==combo[,2])/nrow(combo)